okay, now I have edited and threadmarked the post with instructions.
Now I'm planning to release a playable version of the mod ... hopefully some time this week
I think that once you have them placed from the auto-generated positions, you can edit details in the map editor. It's far easier there and despite the editor being quite unstable, it can be much faster than coding it. But still this work is IMHO a last instance detail you need to do.
Í'm glad it helped. Anyway, the missing positions are and should not be game-breaking, although they generate error logs. And as discussed above, you can still take them from the auto-generated files and copy them where necessary.
Yea I used those files last night and it was far easier with me only having to move the position files around. I loaded up the game opened map editor so it made the generated files then copied the position files over and re-loaded the game. It seems the game does at least do the CK2 thing of auto placing everything in the middle of a province regardless of size when it's generated so I also didn't need to move things from the corner of the map.